Unfortunately Colorado (3-1-1) scored the scrappy goal while Toronto midfielder Kyle Bekker came oh so close to two late moments of brilliance Saturday.
"To tell you the truth, in the second half I thought there was only going to be one team that was going to win that game," said Nelsen. "The cruelty of football isn't it when you hit the post and 30 seconds later they score at the other end."
Former Toronto forward Edson Buddle decided the game with his 99th career MLS goal, from close range in the 77th minute, as the visiting Rapids edged an injury-ridden Toronto side 1-0 before an announced sellout of 22,591.
Colorado, which had been on its heels earlier in the second half, took advantage of a Toronto defensive letdown to secure the three points.
Toronto (3-2-0) was without five starters including star striker Jermain Defoe (hamstring) and midfielder Michael Bradley (quadricep and groin), whose combined salaries are almost US$13 million this season. Also missing were midfielders Jonathan Osorio and Alvaro Rey (both hamstrings) and central defender Doneil Henry (knee).
"I think their depth was tested today," said Colorado defender Drew Moor. "I'd be lying if I said when we saw the team sheet that it didn't make us a little more hungry."
While Nelsen wanted to talk about those players who were on the pitch rather than the ones missing, he couldn't resist point out that any team would struggle without "five very influential players."
"Especially a young team like us."
Adding to Toronto's woes was the fact that attacking midfielder Dwayne De Rosario, who was subbed out in the 67th minute, was walking with a limp after the game with what Nelsen called a muscle injury.
Toronto plays in Dallas next weekend and then has a bye to regroup. The club could well opt to have some of the injured players skip the Dallas game to give them more time to recover.
Bradley had been a question-mark for Saturday and failed to recover in time. Nelsen said Bradley faced being out for "several weeks, pushing on months" if he had played and aggravated his injuries.
The star midfielder played for both the U.S and Toronto last week, with his body paying the price.
Colorado was missing leading scorer Vicente Sanchez, who did not make the trip because his wife is expecting their first child.
The drab game reflected the conditions: grey skies and a stiff wind blowing on a bumpy pitch.
"There was only a few spells of decent soccer being played out there," said Colorado coach Pablo Mastroeni. "The rest of it was grit, rolling up your sleeves, second balls and battles. That's what I said to the guys going in. This game is not going to be about soccer, it's going to be about determination and will and fight and getting those second balls and shielding and putting balls in dangerous spots."
That is exactly how the goal happened. Austrian defender Thomas Piermayr found Dillon Serna in the penalty box with a long ball from the right flank, Serna drove it back into the box, Deshorn Brown got his head to it and the ball found its way back to Serna as the Toronto defence struggled to keep up.
Serna passed to Dillon Powers who drove into the box, attracting two Toronto defenders before raking a short ball back to an unmarked Buddle in front
Seconds earlier, Bekker had bent a free kick round the wall and off the goalpost. Bekker hit the woodwork again in stoppage time.
Asked what he thought after hitting both free kicks, Bekker replied: "Goal."
"I thought he was brilliant today," Nelsen said of the 23-year-old Canadian. "Absolutely brilliant, one of our standout players."
Colorado had lost all six of its previous games at BMO Field against Toronto although it did win the MLS Cup here in 2010, beating FC Dallas.
Toronto's bench was young and green with 18-year-old Jordan Hamilton, 21-year-old Nick Hagglund, 22-year-old Gale Agbossoumonde, 23-year-old Ashtone Morgan, 24-year-old Joe Bendik and Andrew Wiedeman, and 25-year-old Ryan Richter.
Just having Morgan on the bench was a surprise. The fullback was listed as being out with a hip flexor strain, which might explain why he took virtually no part in warmup. Nelsen said later Morgan could not have played, but was on the bench to be part of the team.
The pitch was an improvement from the home opener three weeks ago but still cut up quickly. The bumpy surface and stiff cross-field wind did not help the quality of the game, with giveaways galore early on.
Colorado looked for a patient buildup while Toronto opted for a more direct approach. Neither produced much of note although there were chances as the first half wore on with Colorado recovering from a slow start to come back at the home side.
Gabriel Torres shot wide and Buddle was stopped in close by Toronto 'keeper Julio Cesar. At the other end, a header from a sliding Gilberto was just wide of the post after a nice cross from Mark Bloom.
But for a team missing so many regulars, Toronto kept it together. Bekker looked calm in central midfield and his influence began to grow in the game.
Toronto began to press in the second half. A Mark Bloom cross flew invitingly through the Colorado box. Then a De Rosario header popped just over the bar as Toronto pressed around the 60-minute mark.
Three former TFC players started for Colorado — Nick LaBrocca, Nathan Sturgis, and Buddle — with Marvell Wynne on the bench.
The 32-year-old Buddle played just 10 games for Toronto in 2007, failing to score.
"Bitterly disappointing," was Toronto captain Steven Caldwell's assessment of the game.
"We just feel if we put in performances like that, we're going to win a lot more games than we're going to lose," he added.